Insular microbiogeography

TL;DR

This study applies the insular biogeography theory to microbial genomics, revealing scale-invariant diversity patterns and suggesting a shift from traditional taxonomy to a quasispecies model for microbes.

Contribution

It demonstrates that microbial gene diversity follows a power law related to insular biogeography, extending macroecological principles to microbial genomics.

Findings

Gene discovery increases with genome number as a power law

Microbial diversity exhibits scale invariance down to SNPs

Traditional taxonomy may be replaced by a quasispecies model

Abstract

The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associated hierarchical web of species interdependence. We report a large scale study of microbial diversity that reveals that the cumulative number of genes discovered increases with the number of genomes studied as a simple power law. This result is demonstrated for three different genera comparing over 15,000 isolates. We show that this power law is formally related to the MacArthur-Wilson exponent, suggesting the emerging diversity of microbial genotypes arises because the scale independent behavior first reported by MacArthur and Wilson extends down to the scale of microbes and their genes. Assessing the depth of available whole genome sequences implies a dynamically changing core genome, suggesting that traditional taxonomic classifications should be replaced with a quasispecies model that captures the diversity and dynamic exchange of genes. We report Species population "clouds" in a defined microbiome, with scale invariance extending down to the level of single-nucleotide polymorphisms (SNPs).